It's pretty obivous to spot if you're a normal user of these types of sites.
But administrators usually have no incentive whatsoever to stop it unless the users actually get out the torches and pitchforks, and the administrators themselves are in danger of being called out as supporting this behavior. But in reality it's trivially easy for them to watch for it and stop it if they're interested in it.
I was in charge of a small, niche hobby forum that garnered about 20k visitors per day. Peanuts compared to anything larger, but even we had shills. I would spot it and stop it because I cared about the quality of the discussion far more than the number of posts or visitors.
Digg lost the number one spot because in its revision previously rather than stomping out shilling and vote scamming, Digg attempted to legitimize it and mainstream the sites that previously had engaged in nefarious acts to try to garner traffic.
Users are not innocent in this whole situation either; if they paid attention and reacted appropriately to shills and obvious voting abuse, the administrators would be forced to act responsibly. But users are apathetic most of the time, and often complicit in it.